Sha256: 14aa9d6d25a14a07f520b000becc7a7691bf327e98c87b4cd4062147d6a4d770
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Size: 1.11 KB
Versions: 168
Compression:
Stored size: 1.11 KB
Contents
module Workflow
def nextflow_file(file, name = nil)
file = file + '.nf' unless File.exists?(file) || ! File.exists?(file + '.nf')
file = File.expand_path(file)
name ||= File.basename(file).sub(/\.nf$/,'')
params = Open.read(file).scan(/params\.\w+/).collect{|p| p.split(".").last}.uniq
params.each do |param|
input param, :string
end
task name => :text do
work = file('work')
output = file('output')
profile = config :profile, :nextflow
Misc.in_dir output do
if profile
cmd("nextflow run -work-dir #{work} -name #{clean_name} -ansi-log false -profile #{profile} #{file}", inputs.to_hash.merge('add_option_dashes' => true))
else
cmd("nextflow run -work-dir #{work} -name #{clean_name} -ansi-log false #{file}", inputs.to_hash.merge('add_option_dashes' => true))
end
end
end
end
def nextflow_dir(path)
main = File.join(path, 'main.nf')
nextflow_file main, File.basename(path)
end
def nextflow(path)
if File.directory?(path)
nextflow_dir path
else
nextflow_file path
end
end
end
Version data entries
168 entries across 168 versions & 1 rubygems